I used Affymetrix Genotyping console, which is provided by Affymetrix company, to analyze copy number variation of my cell lines after Genomewide SNP6.0 arrays were used.
Strangely, the number of CN probes is 908043. According to Affymetrix homepage and its annotation file(GenomeWideSNP_6.cn.na35.annot.csv), their number should be 945826 regardless of annotation file's release.
Approximately, 40000 probes were missed. I don't have any idea how to understand this situation.
Are their overlapped probes between CN probes and SNP probes? If there are overlapped probes, where is the information on the overlapped probes?